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Old 06-10-2011, 09:20 AM   #1
salmonella
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Default Filtering and trimming data

Is there a stand alone program (i.e. not incorporated into Velvet, Bowtie etc) that I can use to filter and trim Illumina fastq sequences

thanks
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Old 06-10-2011, 10:30 PM   #2
malcook
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Default fastx toolkit

http://hannonlab.cshl.edu/fastx_toolkit/
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Old 06-11-2011, 02:21 AM   #3
jameslz
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http://edwards.sdsu.edu/prinseq_beta/
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Old 06-11-2011, 12:26 PM   #4
tnabtaf
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While not exactly standalone, there are a bunch filtering and QC options on the public Galaxy server. Go to usegalaxy.org and click on "NGS: QC and manipulation" in the left bar.
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Old 06-11-2011, 02:22 PM   #5
mtmorgan
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R / Bioconductor has flexible tools in the ShortRead, Biostrings, and GenomicRanges packages. Some relevant functions include readFastq, writeFastq, SRFilter, trimLRPatterns, alphabet, alphabetByCycle, narrow, trimTails (in the `devel` branch), ...
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Old 06-13-2011, 09:01 AM   #6
steven
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A new one: Btrim
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Old 06-14-2011, 12:06 AM   #7
sklages
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Quote:
Originally Posted by steven View Post
A new one: Btrim
It would be helpful if these kind of tools would be aware of paired-ends and keep the final output file(s) synced (in terms of of read/mate positions/existence in output).
Just a thought :-)
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Old 11-15-2011, 03:22 AM   #8
pd
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Default TRimming FASTQ file

Dear,

I want to trim my FASTq file (illumina) because of GT contamination in the beginning of every read. SO, my doubt is, When i trim the read sequence from 5' end (Left of the sequence) then do i need to trim the line having qual score as well?

With REgards
Parveen Kumar
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Old 11-15-2011, 03:26 PM   #9
Heisman
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Quote:
Originally Posted by parveendabas View Post
Dear,

I want to trim my FASTq file (illumina) because of GT contamination in the beginning of every read. SO, my doubt is, When i trim the read sequence from 5' end (Left of the sequence) then do i need to trim the line having qual score as well?

With REgards
Parveen Kumar
Yes, that would be correct. Trim the qual score too.
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Old 11-15-2011, 10:18 PM   #10
RockChalkJayhawk
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You should be able to trim reads directly, at least I know you can with Bowtie. Lok at the available options for all these tools.
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Old 11-17-2011, 05:39 AM   #11
pd
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thank you... cheers.
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